One option is to run the Java application in a separate process and use the interprocess communications between the Java application and the C data collector.
As for compiling Java and referencing C, this is possible if your toolbox supports it. For example, if you use the full-featured GNU compiler, gcc and gcj can work together, however you need to understand that Java is not just a language, but also an environment. Doing your own compilation of Java may not give you any reason why you are using Java for the system.
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